I think the issue is your view of the 'third' disk is not what the hardware now knows as disk 3. Windows is not changing anything, the boot.ini is stating the disk and partition layout it knew when installed, it is the PC that has swapped the numbering of the disks since it 'forgot' the values during the battery swap.
Had you removed the SATA drive during the 1st initialisation with the new battery, and then subsequently re-attched, all would be the same.
The difference in labels is less important. The logical disk manager sees 'logical' disks and partitions and dynamically orders these (plug and pray) in XP as they are added. It's not so dynamic in Win2K but still accurate. If you click on the 'disk' details and right-click properties, you should see the specific device info (manuf/model) and what the hardware sees.
HTH.